More ships = more berths for captains.
More ships = more fuel used (possibly).
More ships = more trips to run.
More ships = more wear on components (Okay, that doesn't apply to "civilian" designs, but is worth a note).
Wow, that was quick
Good points, currently I am running squadrons of 5 smaller freighters capable of moving installations in one trip together.
My 35,000 ton freighter design is probably more efficient (fuel, resource use to build, etc).
The idea of flexibility from having multiple smaller freighters is negated by the issue they are needed together in squadrons to move a whole installation in one lift.
Fuel is not really a concern for me at the moment (haven't even left the solar system and there is plentiful sorium)
As for more management of multiple ships it is not too onerous as the smaller freighters are operated together as a squadron.
However my smaller freighters are giving me a useful outlet for Lieutenant Commanders who need their first command.
Thanks for covering some of the issues, I think I may go up to 35,000 tons on one of my civilian shipyards early in the game (and just keep adding slips at another), just not really sure if there are many other needs early on for large shipyards over more slips per shipyard.